This morning I had one of these really fun video-game-like dreams. I was with a large group of other people in a vast flat space dotted with sheds like an abandoned airport or a railyard without the rails. We were running from building to building because a titanic winged alligator snapping turtle kept swooping at us. We could see it circling overhead, silhouetted against the clouds glowing with the light of a city on fire. Its name was the Trypanosome.
Some of us including myself had a special ability . Some of the sheds held vending machines dispensing small red capsules the colour of cinnamon candies. When I took one into my mouth, I felt it become spherical and hot, and I could spit it a great distance. It turned into an acid bomb. So those of uswho had this peculiar offensive capability were trying to bombard the flying turtle and drive it away from the other defenseless humans.
The problem is that we were quickly running out of the acid bombs. Someone discovered another type of vending machine that contained yellow capsules that would let you spit laser beams, but they were low-power lasers so we had to act much more quickly and in concert to protect the others. The Trypanosome sensed that its attackers were weakening, and it was making lower and lower passes over us…
As so often happens with dreams, my alarm went off as it was getting to the exciting bit.

This morning I was chatting with a physician from a Francophone country who’s volunteering at a charity clinic while waiting to pass her exams to practice in South Africa. I asked her what health problems she commonly sees among the clients.
“Scabies, allergic rhinitis, achivey…”
“What’s achivey? I haven’t heard of it before.”
“It’s a virus, it can be sexually transmitted, it cause AIDS.”
“Ohhhhhhhh that’s how you pronounce “H”, “I”, “V” in French!”
😂😂😂😂

Political instability interrupts treatment, facilitates disease spread e.g. strikes in South Africa, post election violence in Kenya, refugees from Syria.
Paradoxical IRIS-like reactions in HIV-negative TB patients.
Why can we not shorten the course of treatment despite the best drugs?
Why do some people not get sick despite similar exposure?
–
Focus on TB in HIV patients in South Africa research may be confounding picture of disease in immunocompetent patients.
Ultra short course phase 3 failure- was based on phase 2 results but phase 2 was underpowered.
Primate models may be more relevant than mouse.
Protection vs exposure- he has not gotten TB but several of his colleagues has. Healthcare workers may be a good cohort to study.
Diagnostic solutions: giant pouched rat (he misspoke as mouse)
Worst case scenario: may have to reopen sanatoria in the absence of effective drugs.

Q&A:
INH prophylaxis lead to resistance?
Ans: if you put a huge cohort of HIV positive patients on prophylaxis, the benefit may outweigh the risk.

GeneXpert does not detect INH resistance, is this a problem?

do you know of any plans to introduce UV in South Africa?
Problem is that it requires good engineering to implement effectively- if not, ineffective, UV burns, etc.
However it could help in combination with other measures e.g. masks. Church of Scotland Hospital study.

What is the fundamental problem of TB in South Africa?
It’s behaviour because we have worse TB rates than poorer African countries like Tanzania.
I am using behaviour in a broad sense – we are doing something wrong. Need to discuss with politicians.

What do u think is the “real” number of people latently infected?
There has not been enough evidence eg strong postmortem study to recover AFB from tissue.

Do u think us in Durban and KZN have some difference from rest of country?
Rest of country is not doing so well either! CPT produces a huge number of TB cases.

me: Boss asked me to get a quote for CO2 from Air Liquide.
Mr Potato: Why? Aren’t we already using Air Liquide?
me: No, all our gas comes from Afrox.
Mr Potato: But Air Liquide is the gold standard in science.
me: WHY DIDN’T YOU TELL ANYBODY THIS EARLIER?
Mr Potato: Because I had no idea we were using Afrox!

Backstory: We’ve been having trouble growing macrophages and Boss is convinced it’s due to the carbon dioxide supply being contaminated with chemicals from the tanks. (Mammalian cells are usually cultured in air with added 5% carbon dioxide.) Mrs. Boss was tasked with putting together some home-made chemical scrubbers, basically, cylinders filled with activated charcoal, but hasn’t gotten around to it for months. Meanwhile Postdoc and I have not been able to do macrophage experiments because they keep dying…

Just thinking about mosquito larvae cos I need to email a Plasmodium guy to ask him to be on my academic committee…

Back in Singapore I kept dwarf pufferfish for a while. They’re really cute and funny little fish, smaller than a marble. They’re also quite aggressive going after any live food that piques their interest, like snails. You won’t have a snail problem with these guys. Continue reading →

It’s March 2015, a crisp Sunday morning in Durban, South Africa, and I am at church. My attention is wandering when suddenly the words “American politics” jolts me back to the sermon. The pastor is illustrating one of his points using the US political system and specific party platforms as an example. I get it, of course. But so does everyone else because they know American politics as well. What could you say about the political system and parties of, say, Canada? South Africa?

Mr Potato has been here for a couple of months now; he sent this email to his former colleagues at Aerospace Company That Shall Not Be Named.

I’ve settled into life in South Africa, with all its ups and downs. Power cuts, theft, and language barriers. That’s just life in Africa. The land here is beautiful, and my wife and I agree that, on the whole, South Africa is more beautiful than any other place we have lived. I think only Ireland is as pretty.

This place is pretty screwed up, though, no way around that. South African natives I meet and hang out with openly admit it. When people hear my American accent, they immediately tell me how much they want to move to America (oh, but that’s a topic deserving its own email later) or anywhere else.

One thing I’ve noticed in South Africa are some of the best public/government Procedures (as opposed to Policy or Processes) anywhere I have lived. The US could learn a thing or two about laws, statutes, and regulation. For example, roads in dark and winding areas have LED lights on the sides of the road to make sure you don’t wander off a hill at night. In a land full of diseases I see posters and other encouragement for good sanitation. Anti-HIV drugs are free to anyone. Immigration laws are actually more concise and navigable than the US.

But this place is profoundly dysfunctional! The laws are world class, why is this place a third world country? Continue reading →

Something woke me up in the middle of the long night. My nose was stuffy and itching. I picked at it for a bit until it felt better and then closed my eyes, wrapping myself against the cold air of the bedroom. Rocking there in the dark, I felt my breathing slow again until a calm oblivion settled into my bones.

It seemed an instant later that I woke again – I knew it must have been some time, but in that dreamless torpor it felt like none. I felt terribly congested now. I sneezed and scratched at my nose, but it would only partially unclog. And as I scraped at it, I realised the horrible sensation of something growing, creeping up my face; a rough hairless texture. I almost screamed. What was I going to do? I couldn’t wipe or scrape it off.

After spending a few minutes silently panicking, I calmed down. Flapping about wouldn’t solve anything. The only thing to do was to go back to sleep and wait for the long night to be over. It’s common sense, I told myself. I’d feel better in the morning.

The next time was worse.

The entire front of my face around my nose and mouth felt like it was burning. My ears had started to itch fiercely as well. Perhaps it was psychological, but something seemed to be wrong with my wing membranes too. Please God, not my wings. There was definitely some kind of crust on my face and the thought of it on my fine, smooth wings made me feel sicker than anything else. I had to stretch at least. Just a few flaps to make sure they were all right.

Close your eyes. Close your eyes, I told myself over and over. Morning had to come.

The next time, I knew it was still too early and worse, with a sinking feeling, that I had already woken up more often than I should. We were still deep into the long night, the night when we should sleep in our big bedroom for months until the cold went away, but my belly and chest already felt too hollow.

The colony stirred. My roost mates were shifting restlessly around me. Some launched off and flapped in circles for a few wingbeats. It was usual that we would wake up now and then, fidget and stretch a little, pee, but then settle down again for the big sleep. Not all of us at once like this, crying and complaining.

I groomed and groomed but couldn’t get the horrible stuff off my wings even though it coated my tongue. Finally I gave up and tried to sleep, willing myself into the depths of unconsciousness against the nagging itch. But even as I wrapped my arms around my body again, I felt the cold consciously, in a way I had not since the first winter without my mother. It would get into my bones and devour me.

I woke up again.

I woke up again. There was very little left.

I woke up again. The urge to move was irresistible. To fly from the pain. I unfurled one wing but it was stiff, the membrane itself swollen thick. I tried to launch but couldn’t get lift and tumbled, like a clumsy baby, to the floor of the bedroom.

The soft thing I landed on was a friend.

The fall hadn’t hurt but I was too exhausted to make the effort of crawling all the way to the wall and climbing back up to any kind of reasonable launch point. I tried to scratch the now all-consuming itch, but only managed to twitch and flail.
The ground shook. The bedroom which had always been our safe space was being invaded by some big animals. From their voices, they were humans, which I had only ever seen from a distance.

There was a white light, and a presence lifted me up.

Backstory: Two days ago I heard a talk on bat physiology and diseases by DeeAnn Reeder, which included an update on the White-Nose Syndrome epizootic in the USA, a fungus imported from Europe which is killing bats by the millions. She showed some microarray data of infected versus uninfected tissue, in addition to a word cloud of keywords related to the upregulated genes (presumably the keywords are based on the homologues of those genes in humans and more familiar mammals). I thought the word cloud/tag cloud was a pretty cool way to show an understandable overview of what was going on, as opposed to a grid of coloured rectangles. But the two big words were “pain” and “itching” and she said that this is how we can guess what the bats feel. It’s haunted me in a way that pictures of the poor things with fungus all over their noses or little dead bodies on the ground don’t.

What flashes before my eyes is not the memories of my life, but Eadward Muybridge’s motion picture, the kinetic series of a galloping horse that proved they take all four feet off the ground. The suspension phase seems to be a suspension of time as well until every violent plunge back down to earth. The world is flying past in a mad rush and slow enough to see the ground beneath our feet at the same time. The right rein that I had accidentally let go of whips around like a snake. I am embarrassingly aware that we are trampling over someone’s young maize crop and terrified that the horse will trip in a furrow, throw me off and kill me.
We were on our way back to the hotel and with the tour guide’s permission I wanted to canter a little across a straight flat part of the track, putting the beginner lessons I took in Colorado to good use. My rented Basotho pony apparently thought he hadn’t had enough exercise in a while and took off. Which was fine until I lost my grip on the right rein and couldn’t hold him in – pulling on the left (obviously, in hindsight) only steered him off the path.
My hands have his mane in a death grip but he is going so fast I’m afraid it will not be enough. In my head I hear my trainer’s voice, the stentor of someone used to calling instructions across an arena – “Knees, knees” – and embrace the horse with my legs. Thank you Stefanie. A few seconds later I realise he’s heading up a hill and surely will have to slow down. I take advantage and finally recapture the right rein, just in time to stop him running down the other side of the hill.
I turn him around and, even panting as he is, have to keep holding him in from starting back the way we came. In the distance are the guide and my flatmate’s friend. I try to wave as best as I can and shout “I am fine.” The guide trots up the hill to us quickly. “Are you all right?”
“I am fine,” I repeat.
“I was so scared,” he says. I understand very well. He would probably have gotten into big trouble if anything happened to a guest, regardless of whether it was the guest’s fault for making noob mistakes.
“I’m really sorry,” I say. “It was an accident. He ran and I couldn’t hold him.”
“You are a one hundred percent good rider,” he says. “Were you not scared?”
“A bit scared,” I say. “I am fine now.”
We walk our horses back down to the path where David waits, me leaning back with the reins in an iron grip all the way. Silly animal.
I know why he ran away. For one glorious minute, we were flying over the black and green mountain fields. I didn’t do it on purpose. But I would do it again.